Issues related to HOMER

Question

[pinky_pinkpinky]

Hi all,

Can any one help me in resolving this issues.

While creating the Tag directory I got this problem.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Average reads per BED file: 255.0
Good chance that the 5th column of your BED file has a weird value in it!
By default, this is read as the number of reads for that position
To count each entry as only one read (ignore the 5th column) use -forceBED
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

    Optimizing tag files...
    Optimizing single genome.tags.tsv file...
    Estimated genome size = 2911405191
    Total Tags = 6130413690.0
    Total Positions = 17702615
    Average tag length = 50.0
    Median tags per position = 255 (ideal: 1)
    Average tags per position = 346.300
        !! Might have some clonal amplification in this sample if sonication was used
        If this is ChIP-Seq using sonicated fragments, consider adding the option "-tbp 1"
        Ignore if analyzing RNA, MNase, etc. data
    Fragment Length Estimate: 103
    Peak Width Estimate: 10
        !!! No reliable estimate for peak size
        Setting Peak width estimate to be equal to fragment length estimate
    Autocorrelation quality control metrics:
        Same strand fold enrichment: 1.1
        Diff strand fold enrichment: 1.1
        Same / Diff fold enrichment: 1.0

        Guessing sample is ChIP-Seq - may have low enrichment with lots of background

When I tried fixing it using force5th I am still getting the same error and I am not getting the Autocorrelation properly while doing the plot.

Thanks

[Istvan Albert]

from your question it is not clear what you think that the problem is

[pinky_pinkpinky]

Hi

The issue is I am not getting the autocorrelation image as its generated in HOMER.

Instead of a distribution plot which gives relative distance between the reads generated through HOMER, I am getting a perpendicular line.

When I checked the values in the tagAutocorrelation.txt file I found at 0th position under ( Distance in bp(Fragment Length Estimate: 120)(Peak Width Estimate: 120)) the values for the in the Same strand and opposite strand is 4739956.0 137976.0 respectively.

Generally the Same strand value is 0 with the kind of analysis I have done so far.

So why I am getting this huge value?

Secondly When I removed this value and made it 0, I could generate the correlation plot.

Why is it coming like this.

Thanks

Answer 1

[pinky_pinkpinky]

Hi

The issue is I am not getting the autocorrelation image as its generated in HOMER.

Instead of a distribution plot which gives relative distance between the reads generated through HOMER, I am getting a perpendicular line.

When I checked the values in the tagAutocorrelation.txt file I found at 0th position under ( Distance in bp(Fragment Length Estimate: 120)(Peak Width Estimate: 120)) the values for the in the Same strand and opposite strand is 4739956.0 137976.0 respectively.

Generally the Same strand value is 0 with the kind of analysis I have done so far.

So why I am getting this huge value?

Secondly When I removed this value and made it 0, I could generate the correlation plot.

Why is it coming like this.

Thanks